[ { "@id": "https://w3id.org/np/RAx-VKIC10JIQnLYqLU8GgBbeAMogA9yngncrRDelWRLU/assertion", "@graph": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium", "@type": [ "http://www.w3.org/ns/prov#SoftwareAgent" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "delphisci dataset-resolvability assessor (Gemini 4 Argon)" } ], "http://www.w3.org/ns/prov#actedOnBehalfOf": [ { "@id": "https://orcid.org/0009-0007-4948-9192" } ], "https://w3id.org/delphi/ontology/usesModel": [ { "@id": "https://w3id.org/delphi/resource/model/gemini-4-argon-medium" } ] }, { "@id": "https://w3id.org/delphi/resource/model/gemini-4-argon-medium", "http://purl.org/dc/terms/identifier": [ { "@value": "gemini-4-argon-medium" } ], "@type": [ "https://w3id.org/delphi/ontology/LanguageModel" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Gemini 4 Argon" } ] }, { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2009-tropocollagen-sequencing-03--gemini", "http://purl.org/dc/terms/description": [ { "@value": "Non-linear, strain-dependent elasticity of single tropocollagen molecules is a well-defined mechanical property that can be tested both by re-running atomistic pulling simulations and by analyzing published optical-tweezers and AFM force-extension data in the literature. While the overall strain-hardening behavior is readily verifiable, testing the full interaction between specific amino-acid sequence motifs and applied deformation state remains partially limited by the lack of a unified repository of sequence-resolved single-molecule force curves." } ], "http://purl.org/dc/terms/subject": [ { "@id": "https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0" } ], "@type": [ "https://w3id.org/delphi/ontology/LLMClaimAssessment" ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "Proposed test with existing data: Fit tangent modulus as a function of applied strain (or force) to published single-molecule optical-tweezers/AFM force-extension curves of type I tropocollagen and to steered MD trajectories across multiple sequence segments, confirming the claim if the tangent modulus changes systematically across low-strain entropic, medium-strain uncoiling, and high-strain backbone-stretching regimes." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Gemini 4 Argon on buehler-2009-tropocollagen-sequencing-03: partially-resolvable, resolvability 0.76" } ], "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium" } ], "https://w3id.org/delphi/ontology/assessmentType": [ { "@value": "dataset-resolvability/0.2.0" } ], "https://w3id.org/delphi/ontology/evidenceAgainst": [ { "@value": "High pulling speeds in atomistic MD shift the apparent strain thresholds at which stiffening and uncoiling occur compared to quasi-static experiments." }, { "@value": "Single-molecule force spectroscopy curves of collagen are scattered across published figures rather than curated in a single standardized open database." } ], "https://w3id.org/delphi/ontology/hasConfidence": [ { "@value": "0.82", "@type": "http://www.w3.org/2001/XMLSchema#double" } ], "https://w3id.org/delphi/ontology/hasEvidence": [ { "@id": "https://w3id.org/delphi/resource/evidence/buehler-2009-tropocollagen-sequencing-03--gemini--dataset-1" }, { "@id": "https://w3id.org/delphi/resource/evidence/buehler-2009-tropocollagen-sequencing-03--gemini--dataset-2" }, { "@id": "https://w3id.org/delphi/resource/evidence/buehler-2009-tropocollagen-sequencing-03--gemini--dataset-3" } ], "https://w3id.org/delphi/ontology/hasScore": [ { "@value": "0.762", "@type": "http://www.w3.org/2001/XMLSchema#double" } ], "https://w3id.org/delphi/ontology/hasVerdict": [ { "@value": "partially-resolvable" } ] }, { "@id": "https://w3id.org/delphi/resource/evidence/buehler-2009-tropocollagen-sequencing-03--gemini--dataset-1", "http://purl.org/dc/terms/description": [ { "@value": "Collagen triple-helix structures for initializing atomistic pulling simulations across low to high strain regimes" } ], "@type": [ "https://w3id.org/delphi/ontology/EvidenceItem" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Candidate dataset: RCSB Protein Data Bank" } ], "http://www.w3.org/ns/prov#wasDerivedFrom": [ { "@id": "https://www.rcsb.org/" } ] }, { "@id": "https://w3id.org/delphi/resource/evidence/buehler-2009-tropocollagen-sequencing-03--gemini--dataset-2", "http://purl.org/dc/terms/description": [ { "@value": "Reference sequences for human type I collagen chains used to parameterize sequence-specific segments" } ], "@type": [ "https://w3id.org/delphi/ontology/EvidenceItem" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Candidate dataset: UniProt Knowledgebase" } ], "http://www.w3.org/ns/prov#wasDerivedFrom": [ { "@id": "https://www.uniprot.org/" } ] }, { "@id": "https://w3id.org/delphi/resource/evidence/buehler-2009-tropocollagen-sequencing-03--gemini--dataset-3", "http://purl.org/dc/terms/description": [ { "@value": "Open molecular dynamics suite to compute force-extension curves and strain-dependent tangent moduli of tropocollagen" } ], "@type": [ "https://w3id.org/delphi/ontology/EvidenceItem" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Candidate dataset: GROMACS" } ], "http://www.w3.org/ns/prov#wasDerivedFrom": [ { "@id": "https://www.gromacs.org/" } ] }, { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2009-tropocollagen-sequencing-03--gemini--analysis-feasibility", "http://purl.org/dc/terms/isPartOf": [ { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2009-tropocollagen-sequencing-03--gemini" } ], "http://purl.org/dc/terms/subject": [ { "@id": "https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0-analysis-feasibility" } ], "@type": [ "https://w3id.org/delphi/ontology/LLMClaimAssessment" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Analysis feasibility of buehler-2009-tropocollagen-sequencing-03 by Gemini 4 Argon: 0.8" } ], "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium" } ], "https://w3id.org/delphi/ontology/assessmentType": [ { "@value": "dataset-resolvability/0.2.0/analysis-feasibility" } ], "https://w3id.org/delphi/ontology/hasScore": [ { "@value": "0.8", "@type": "http://www.w3.org/2001/XMLSchema#double" } ] }, { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2009-tropocollagen-sequencing-03--gemini--data-adequacy", "http://purl.org/dc/terms/isPartOf": [ { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2009-tropocollagen-sequencing-03--gemini" } ], "http://purl.org/dc/terms/subject": [ { "@id": "https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0-data-adequacy" } ], "@type": [ "https://w3id.org/delphi/ontology/LLMClaimAssessment" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Data adequacy of buehler-2009-tropocollagen-sequencing-03 by Gemini 4 Argon: 0.68" } ], "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium" } ], "https://w3id.org/delphi/ontology/assessmentType": [ { "@value": "dataset-resolvability/0.2.0/data-adequacy" } ], "https://w3id.org/delphi/ontology/hasScore": [ { "@value": "0.68", "@type": "http://www.w3.org/2001/XMLSchema#double" } ] }, { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2009-tropocollagen-sequencing-03--gemini--data-existence", "http://purl.org/dc/terms/isPartOf": [ { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2009-tropocollagen-sequencing-03--gemini" } ], "http://purl.org/dc/terms/subject": [ { "@id": "https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0-data-existence" } ], "@type": [ "https://w3id.org/delphi/ontology/LLMClaimAssessment" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Data existence of buehler-2009-tropocollagen-sequencing-03 by Gemini 4 Argon: 0.72" } ], "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium" } ], "https://w3id.org/delphi/ontology/assessmentType": [ { "@value": "dataset-resolvability/0.2.0/data-existence" } ], "https://w3id.org/delphi/ontology/hasScore": [ { "@value": "0.72", "@type": "http://www.w3.org/2001/XMLSchema#double" } ] }, { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2009-tropocollagen-sequencing-03--gemini--discriminating-power", "http://purl.org/dc/terms/isPartOf": [ { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2009-tropocollagen-sequencing-03--gemini" } ], "http://purl.org/dc/terms/subject": [ { "@id": "https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0-discriminating-power" } ], "@type": [ "https://w3id.org/delphi/ontology/LLMClaimAssessment" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Discriminating power of buehler-2009-tropocollagen-sequencing-03 by Gemini 4 Argon: 0.78" } ], "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium" } ], "https://w3id.org/delphi/ontology/assessmentType": [ { "@value": "dataset-resolvability/0.2.0/discriminating-power" } ], "https://w3id.org/delphi/ontology/hasScore": [ { "@value": "0.78", "@type": "http://www.w3.org/2001/XMLSchema#double" } ] }, { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2009-tropocollagen-sequencing-03--gemini--operationalizability", "http://purl.org/dc/terms/isPartOf": [ { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2009-tropocollagen-sequencing-03--gemini" } ], "http://purl.org/dc/terms/subject": [ { "@id": "https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0-operationalizability" } ], "@type": [ "https://w3id.org/delphi/ontology/LLMClaimAssessment" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Operationalizability of buehler-2009-tropocollagen-sequencing-03 by Gemini 4 Argon: 0.85" } ], "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium" } ], "https://w3id.org/delphi/ontology/assessmentType": [ { "@value": "dataset-resolvability/0.2.0/operationalizability" } ], "https://w3id.org/delphi/ontology/hasScore": [ { "@value": "0.85", "@type": "http://www.w3.org/2001/XMLSchema#double" } ] }, { "@id": "https://w3id.org/delphi/resource/claim/buehler-2009-tropocollagen-sequencing-03", "https://w3id.org/delphi/ontology/hasAssessment": [ { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2009-tropocollagen-sequencing-03--gemini" }, { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2009-tropocollagen-sequencing-03--gemini--analysis-feasibility" }, { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2009-tropocollagen-sequencing-03--gemini--data-adequacy" }, { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2009-tropocollagen-sequencing-03--gemini--data-existence" }, { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2009-tropocollagen-sequencing-03--gemini--discriminating-power" }, { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2009-tropocollagen-sequencing-03--gemini--operationalizability" } ] } ] }, { "@id": "https://w3id.org/np/RAx-VKIC10JIQnLYqLU8GgBbeAMogA9yngncrRDelWRLU/provenance", "@graph": [ { "@id": "https://w3id.org/np/RAx-VKIC10JIQnLYqLU8GgBbeAMogA9yngncrRDelWRLU/assertion", "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium" } ], "http://www.w3.org/ns/prov#wasDerivedFrom": [ { "@id": "https://github.com/fractastical/delphisci/blob/67fe5b156cfeca15a2ded33e0face4177d03101c/claim-sources/buehler-protein-materials/assessment/raw/gemini/batch-4.json" }, { "@id": "https://w3id.org/delphi/resource/concept/dataset-resolvability-0.2.0" } ], "http://www.w3.org/ns/prov#wasGeneratedBy": [ { "@id": "https://w3id.org/np/RAx-VKIC10JIQnLYqLU8GgBbeAMogA9yngncrRDelWRLU/assessment" } ] }, { "@id": "https://w3id.org/np/RAx-VKIC10JIQnLYqLU8GgBbeAMogA9yngncrRDelWRLU/assessment", "@type": [ "http://www.w3.org/ns/prov#Activity" ], "http://www.w3.org/ns/prov#qualifiedAssociation": [ { "@id": "https://w3id.org/np/RAx-VKIC10JIQnLYqLU8GgBbeAMogA9yngncrRDelWRLU/assessmentPlan" } ], "http://www.w3.org/ns/prov#wasAssociatedWith": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-resolvability-assessor-gemini-4-argon-medium" } ] }, { "@id": "https://w3id.org/np/RAx-VKIC10JIQnLYqLU8GgBbeAMogA9yngncrRDelWRLU/assessmentPlan", "http://www.w3.org/ns/prov#hadPlan": [ { "@id": "https://github.com/fractastical/delphisci/blob/67fe5b156cfeca15a2ded33e0face4177d03101c/claim-sources/buehler-protein-materials/README.md" } ] } ] }, { "@id": "https://w3id.org/np/RAx-VKIC10JIQnLYqLU8GgBbeAMogA9yngncrRDelWRLU/pubinfo", "@graph": [ { "@id": "https://w3id.org/delphi/resource/domain/buehler-protein-materials", "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "buehler-protein-materials" } ] }, { "@id": "https://w3id.org/np/RAx-VKIC10JIQnLYqLU8GgBbeAMogA9yngncrRDelWRLU", "http://purl.org/dc/terms/created": [ { "@value": "2026-11-08T04:48:50.317Z", "@type": "http://www.w3.org/2001/XMLSchema#dateTime" } ], "http://purl.org/dc/terms/creator": [ { "@id": "https://orcid.org/0009-0007-4948-9192" } ], "http://purl.org/dc/terms/license": [ { "@id": "https://creativecommons.org/licenses/by/4.0/" } ], "http://purl.org/nanopub/x/hasNanopubType": [ { "@id": "https://w3id.org/delphi/ontology/LLMClaimAssessment" } ], "http://purl.org/nanopub/x/introduces": [ { "@id": "https://w3id.org/delphi/resource/assessment/buehler-2009-tropocollagen-sequencing-03--gemini" } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Gemini 4 Argon on buehler-2009-tropocollagen-sequencing-03: partially-resolvable, resolvability 0.76" } ], "https://w3id.org/delphi/ontology/domain": [ { "@id": "https://w3id.org/delphi/resource/domain/buehler-protein-materials" } ] }, { "@id": "https://w3id.org/np/RAx-VKIC10JIQnLYqLU8GgBbeAMogA9yngncrRDelWRLU/sig", "http://purl.org/nanopub/x/hasAlgorithm": [ { "@value": "RSA" } ], "http://purl.org/nanopub/x/hasPublicKey": [ { "@value": "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAyFHtPB6p0mCjDozxlOY9CmO3nBm7Te3jFbXyLmM+G1tGe47Da0jYIbhkl9Oo1ZjxmCa3LCwlEqK8gj6hEIcL4ahW30JXh9HycfKVk1bugkzMEV15tJdTzAU3sGMFnbNsn43xY2LFLy45tApkRm5byEiM7oRRrooIdwoQKnP4Wzq/bfAoJ9qvW+MGkelyOTd1jbSt+KfmT7xKmDfWzAHddUlWwMX2QJOLxDaffOteTop6ZRgPiNmPJKA/S62Gac9XtSYT3oDkZ6/nr5cxxNLpOyxTf5FPISiCe11xYO/unYjY+mwnOfA8yhJIyx1l0O9I0vpOpn+E5TvyHJV+oSTrvwIDAQAB" } ], "http://purl.org/nanopub/x/hasSignature": [ { "@value": "w+hk5/8ozT1CCDe+qpXuD1gEGRxGzQP0oS5rtY08i7zaTDKpKs3s52ezLv13Gn8Hc3IbC8wy2nZjz51PIyVANH9PDofKma49H978NWQw/9MO+PkNk3XpJhsKPYxBTXjCeG8vkt1viHi7dB9z2o2SwCFqOEkTbJH9cFf8+I8XXOmHx88o3FRqr4zxsfboiTVkCWJiu2ilE5srY40XoiSYFmPMbav+xhP0NQeZXwu0n3stdwGsu+Kq9TfH2YdVibUymD1q/KpDzqq89nEhloISJbyhtDi8EJ3pNgFLOGZV3uyhDUZfgGdccYNxk/95rKQWfZ09my954Sav7hhg+f+86Q==" } ], "http://purl.org/nanopub/x/hasSignatureTarget": [ { "@id": "https://w3id.org/np/RAx-VKIC10JIQnLYqLU8GgBbeAMogA9yngncrRDelWRLU" } ], "http://purl.org/nanopub/x/signedBy": [ { "@id": "https://orcid.org/0009-0007-4948-9192" } ] } ] }, { "@id": "https://w3id.org/np/RAx-VKIC10JIQnLYqLU8GgBbeAMogA9yngncrRDelWRLU/Head", "@graph": [ { "@id": "https://w3id.org/np/RAx-VKIC10JIQnLYqLU8GgBbeAMogA9yngncrRDelWRLU", "http://www.nanopub.org/nschema#hasAssertion": [ { "@id": "https://w3id.org/np/RAx-VKIC10JIQnLYqLU8GgBbeAMogA9yngncrRDelWRLU/assertion" } ], "http://www.nanopub.org/nschema#hasProvenance": [ { "@id": "https://w3id.org/np/RAx-VKIC10JIQnLYqLU8GgBbeAMogA9yngncrRDelWRLU/provenance" } ], "http://www.nanopub.org/nschema#hasPublicationInfo": [ { "@id": "https://w3id.org/np/RAx-VKIC10JIQnLYqLU8GgBbeAMogA9yngncrRDelWRLU/pubinfo" } ], "@type": [ "http://www.nanopub.org/nschema#Nanopublication" ] } ] } ]